| 1. |
- Aaltonen, Kristina, et al.
(författare)
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Molecular Population Genetics of the SRK and SCR Self-incompatibility Genes in the Wild Plant Species Brassica cretica (Brassicaceae).
- 2009
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 181:3, s. 985-995
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Tidskriftsartikel (refereegranskat)abstract
- Self-incompatibility (SI) in plants is a classic example of a trait evolving under strong frequency-dependent selection. As a consequence, population genetic theory predicts that the S locus, which controls SI, should maintain numerous alleles, display a high level of nucleotide diversity, and, in structured populations, show a lower level of among-population differentiation compared to neutral loci. Population-level investigations of DNA sequence variation at the S locus have recently been carried out in the genus Arabidopsis, largely confirming results from theoretical models of S-locus evolutionary dynamics, but no comparable studies have been done in wild Brassica species. In this study, we sequenced parts of the S-locus genes SRK and SCR, two tightly linked genes that are directly involved in the determination of SI specificity, in samples from four natural populations of the wild species Brassica cretica. The amount and distribution of nucleotide diversity, as well as the frequency spectrum of putative functional haplotypes, observed at the S locus in B. cretica fit very well with expectations from theoretical models, providing strong evidence for frequency-dependent selection acting on the S locus in a wild Brassica species.
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| 2. |
- Aaltonen, Kristina, et al.
(författare)
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The Evolution and Diversification of S-locus Haplotypes in the Brassicaceae Family.
- 2009
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 181:3, s. 977-984
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Tidskriftsartikel (refereegranskat)abstract
- Self-incompatibility (SI) in the Brassicaceae plant family is controlled by the SRK and SCR genes situated at the S locus. A large number of S haplotypes have been identified, mainly in cultivated species of the Brassica and Raphanus genera, but recently also in wild Arabidopsis species. Here, we used DNA sequences from the SRK and SCR genes of the wild Brassica species B. cretica, together with publicly available sequence data from other Brassicaceae species, to investigate the evolutionary relationships between S haplotypes in the Brassicaceae family. The results reveal that wild and cultivated Brassica species have similar levels of SRK diversity indicating that domestication has had but a minor effect on S-locus diversity in Brassica. Our results also show that a common set of S haplotypes were present in the ancestor of the Brassica and Arabidopsis genera, that only a small number of haplotypes survived in the Brassica lineage after its separation from Arabidopsis, and that diversification within the two Brassica dominance classes occurred after the split between the two lineages. We also find indications that recombination may have occurred between the kinase domain of SRK and the SCR gene in Brassica.
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| 3. |
- Albert, Frank W., et al.
(författare)
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Genetic architecture of tameness in a rat model of animal domestication
- 2009
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 182:2, s. 541-554
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Tidskriftsartikel (refereegranskat)abstract
- A common feature of domestic animals is tameness - i.e., they tolerate and are unafraid of human presence and handling. To gain insight into the genetic basis of tameness and aggression, we studied an intercross between two lines of rats (Rattus norvegicus) selected over >60 generations for increased tameness and increased aggression against humans, respectively. We measured 45 traits, including tameness and aggression, anxiety-related traits, organ weights, and levels of serum components in >700 rats from an intercross population. Using 201 genetic markers, we identified two significant quantitative trait loci (QTL) for tameness. These loci overlap with QTL for adrenal gland weight and for anxiety-related traits and are part of a five-locus epistatic network influencing tameness. An additional QTL influences the occurrence of white coat spots, but shows no significant effect on tameness. The loci described here are important starting points for finding the genes that cause tameness in these rats and potentially in domestic animals in general.
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| 4. |
- Álvarez-Castro, José M., et al.
(författare)
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A unified model for functional and statistical epistasis and its application in quantitative trait loci analysis
- 2007
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 176:2, s. 1151-1167
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Tidskriftsartikel (refereegranskat)abstract
- Interaction between genes, or epistasis, is found to be common and it is a key, concept for understanding adaptation and evolution of natural populations, response to selection in breeding programs, and determination of complex disease. Current]),, two independent classes of models are used to study epistasis. Statistical models focus on maintaining desired statistical properties for detection and estimation of genetic effects and for the decomposition of genetic variance using average effects of allele Substitutions in populations as parameters. Functional models focus on the evolutionary consequences of the attributes of the genotype-phenotype map using natural effects of allele substitutions as parameters. Here we provide a new, general and unified model framework: the natural and orthogonal interactions (NOIA) model. NOIA implements tools for transforming genetic effects measured in One Population to the ones of other populations (e.g., between two experimental designs for QTL) and parameters of statistical and functional epistasis into each other (thus enabling us to obtain functional estimates of QTL), as demonstrated numerically. We develop graphical interpretations of functional and statistical models as regressions of the genotypic values on the gene content, which illustrates the difference between the models-the constraint on the slope of the functional regression-and when the models are equivalent. Furthermore, we use our theoretical foundations to conceptually clarify functional and statistical epistasis, discuss the advantages of NOIA over previous theory, and stress the importance of linking functional and statistical models.
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| 5. |
- Backström, Niclas, et al.
(författare)
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A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution
- 2008
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 179, s. 1479-1495
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Tidskriftsartikel (refereegranskat)abstract
- By taking advantage of a recently developed reference markerset for avian genome analysis we have constructed a gene-basedgenetic map of the collared flycatcher, an important "ecologicalmodel" for studies of life-history evolution, sexual selection,speciation, and quantitative genetics. A pedigree of 322 birdsfrom a natural population was genotyped for 384 single nucleotidepolymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites.Altogether, 147 gene markers and 64 microsatellites form 33linkage groups with a total genetic distance of 1787 cM. Malerecombination rates are, on average, 22% higher than femalerates (total distance 1982 vs. 1627 cM). The ability to anchorthe collared flycatcher map with the chicken genome via thegene-based SNPs revealed an extraordinary degree of both syntenyand gene-order conservation during avian evolution. The greatmajority of chicken chromosomes correspond to a single linkagegroup in collared flycatchers, with only a few cases of inter-and intrachromosomal rearrangements. The rate of chromosomaldiversification, fissions/fusions, and inversions combined isthus considerably lower in birds (0.05/MY) than in mammals (0.6–2.0/MY).A dearth of repeat elements, known to promote chromosomal breakage,in avian genomes may contribute to their stability. The degreeof genome stability is likely to have important consequencesfor general evolutionary patterns and may explain, for example,the comparatively slow rate by which genetic incompatibilityamong lineages of birds evolves.
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| 6. |
- Backström, Niclas, et al.
(författare)
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Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis) : Conserved synteny but gene order rearrangements on the avian Z chromosome
- 2006
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 174:1, s. 377-386
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Tidskriftsartikel (refereegranskat)abstract
- Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher-one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only similar to 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.
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| 7. |
- Barsoum, Emad, 1979-, et al.
(författare)
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Ume6 is required for the MATa/MATα cellular identity and transcriptional silencing in Kluyveromyces lactis
- 2010
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Ingår i: Genetics. - : The Genetics Society of America. - 0016-6731 .- 1943-2631. ; 184:4, s. 999-1011
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Tidskriftsartikel (refereegranskat)abstract
- To explore the similarities and differences of regulatory circuits among budding yeasts, we characterized the role of the unscheduled meiotic gene expression 6 (UME6) gene in Kluyveromyces lactis. We found that Ume6 was required for transcriptional silencing of the cryptic mating-type loci HMLα and HMRa. Chromatin immunoprecipitation (ChIP) suggested that Ume6 acted directly by binding the cis-regulatory silencers of these loci. Unexpectedly, a MATa ume6 strain was mating proficient, whereas a MATα ume6 strain was sterile. This observation was explained by the fact that ume6 derepressed HMLα2 only weakly, but derepressed HMRa1 strongly. Consistently, two a/α-repressed genes (MTS1 and STE4) were repressed in the MATα ume6 strain, but were expressed in the MATa ume6 strain. Surprisingly, ume6 partially suppressed the mating defect of a MATa sir2 strain. MTS1 and STE4 were repressed in the MATa sir2 ume6 double-mutant strain, indicating that the suppression acted downstream of the a1/α2-repressor. We show that both STE12 and the MATa2/HMRa2 genes were overexpressed in the MATa sir2 ume6 strain. Consistent with the idea that this deregulation suppressed the mating defect, ectopic overexpression of Ste12 and a2 in a MATa sir2 strain resulted in efficient mating. In addition, Ume6 served as a block to polyploidy, since ume6/ume6 diploids mated as pseudo a-strains. Finally, Ume6 was required for repression of three meiotic genes, independently of the Rpd3 and Sin3 corepressors.
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| 8. |
- Bengtsson, Bengt Olle
(författare)
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Asexuals, Polyploids, Evolutionary Opportunists ...: The Population Genetics of Positive but Deteriorating Mutations.
- 2012
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 191:4, s. 499-1393
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Tidskriftsartikel (refereegranskat)abstract
- Some genetic phenomena originate as mutations that are initially advantageous but decline in fitness until they become distinctly deleterious. Here I give the condition for a mutation-selection balance to form and describe some of the properties of the resulting equilibrium population. A characterization is also given of the fixation probabilities for such mutations.
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| 9. |
- Bengtsson, Bengt Olle, et al.
(författare)
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The 1948 international congress of genetics in Sweden: People and politics.
- 2010
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Ingår i: Genetics. - : Oxford University Press (OUP). - 0016-6731 .- 1943-2631. ; 185:3, s. 709-715
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Tidskriftsartikel (refereegranskat)abstract
- The International Congresses have played an important role in the history of genetics. The Eighth International Congress, which in 1948 was held in Sweden, celebrated the conclusion of the war against Nazism and many new decisive scientific advances. It also signaled a hardening of the fight against Lysenkoism, which was growing in strength in the Soviet Union. A rare document is available from the Congress-an amateur film made by a young delegate, Nils Nybom. With its help a living description can be given of the scientific and political melees in which the delegates were involved.
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| 10. |
- Berg, OG
(författare)
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Selection intensity for codon bias and the effective population size of Escherichia coli
- 1996
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Ingår i: GENETICS. - : GENETICS. - 0016-6731. ; 142:4, s. 1379-1382
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The selection intensity for codon bias and the synonymous diversity have been used in the recent literature to estimate the effective population size of Escherichia coli. The results have varied between 10(5) and 10(8). It is suggested here that most of t
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